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Van Cise AM, Switzer AD, Apprill A, Champagne CD, Chittaro PM, Dudek NK, Gavery MR, Hancock‐Hanser BL, Harmon AC, Jaffe AL, Kellar NM. 2024. Best practices for collecting and preserving marine mammal biological samples in the ‘omics era. Marine Mammal Science. e13148. Open Access

Garcia BM, Becker CC, Weber L, Swarr GJ, Kido Soule MC, Apprill A, Kujawinski EB. 2024. Benzoyl Chloride Derivatization Advances the Quantification of Dissolved Polar Metabolites on Coral Reefs. Journal of Proteome Research. 23, 6, 2041–2053.  Press Release  Link to article

Aoki N, Weiss B, Jézéquel Y, Zhang WG, Apprill A, Mooney TA. Soundscape enrichment increases larval settlement rates for the brooding coral Porites astreoides. 2024. Royal Society Open Science. 11(3):231514. Open Access  Press Release

Marzo-Pérez D, Pérez-García JA, Apprill A, Armenteros M. Diversity of Cryptofaunal Nematode Assemblages along the Jardines de La Reina Coral Reef, Southern Cuba. 2024. Diversity. 16(5):264.  Open Access

Becker CC, Weber L, Llopiz JK, Mooney TA, Apprill A. 2024. Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs. Environmental Microbiology. 16:4. Open Access    Press Release

Jarriel SD, Formel N, Ferguson SR, Jensen FH, Apprill A, Mooney TA. Unidentified fish sounds as indicators of coral reef health and comparison to other acoustic methods. Frontiers in Remote Sensing. 5, 1338586. Open Access

Pereira A, Brown A, Strobel D, Soares MC, Xavier R, Apprill A, Sikkel P. 2024. Effects of two common antibiotics on the skin microbiome of ornamental reef fishes: implications for manipulative experiments in microbial dynamics, Aquaculture, Fish and Fisheries. 4 (3), e162.  Open Access

Reigel AM, Easson CG, Apprill A, Freeman CJ, Bartley MM, Fiore CL. 2024. Sponge-derived matter is assimilated by coral holobionts. Communications Biology. 7(1), 146.  Open Access


Sun Y, Mazzotta MG, Miller CA, Apprill A, Izallalen M, Mazumder S, Perri ST, Edwards B, Reddy CM, Ward CP. 2023. Distinct microbial communities degrade cellulose diacetate bioplastics in the coastal ocean. Applied and Environmental Microbiology. e01651-23.

Becker CC, Weber L, Zgliczynski B, Sullivan C, Sandin S, Muller E, Clark AS, Kido Soule MC, Longnecker K, Kujawinski EB, Apprill A. 2023. Microorganisms and dissolved metabolites distinguish Florida’s coral reef habitats. PNAS nexus:pgad287. Open Access  Press Release

Beavers KM, Van Buren EW, Rossin AM, Emery MA, Veglia AJ, Karrick CE, MacKnight NJ, Dimos BA, Meiling SS, Smith TB, Apprill A, Muller EM, Holstein DM, Correa AMS, Brandt ME, Mydlarz LD. 2023. Stony coral tissue loss disease induces transcriptional signatures of in situ degradation of dysfunctional Symbiodiniaceae. Nature Communications. 14(1):2915.  Open Access

Lillis A, Apprill A, Armenteros A, Mooney T. 2023. Small scale variation in the soundscapes of coral reefs. In: The Effects of Noise on Aquatic Life: Principles and Practical Considerations. Edited by Arthur N. Popper, Joseph Sisneros, Anthony Hawkins, and Frank Thomsen. Springer.

Cayemitte K, Aoki N, Ferguson SR, Mooney TA, Apprill A. 2023. Ramicrusta invasive alga causes mortality in Caribbean coral larvae. Frontiers in Marine Science. 10:663. Open Access

Apprill A, Girdhar Y, Mooney TA, Hansel CM, Long MH, Liu Y, Zhang WG, Kapit J, Hughen K, Coogan J, Greene A. 2023. Toward a new era of coral reef monitoring. Environmental Science & Technology. 57(13):5117-5124.  Open Access   Cover Image    Press Release

Rosales SM, Huebner LK, Evans JS, Apprill A, Baker AC, Becker CC, Bellantuono AJ, Brandt ME, Clark AS, Del Campo J, Dennison CE, Eaton KR, Huntley NE, Kellogg CA, Medina M, Meyer JL, Muller EM, Rodriguez-Lanetty M, Salerno JL, Schill WB, Shilling EN, Stewart JM, Voss JD. 2023. A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in unaffected and lesion tissue in diseased colonies. ISME Communications 3:19. Open Access


Brown A, Sharp K, Apprill A. 2022. Reshuffling of the coral microbiome during dormancy. Applied and Environmental Microbiology. 88: e01391-22. Open Access    Press Release

Weber L, Soule MK Longnecker K, Becker CC, Huntley N, Kujawinski EB, Apprill A. 2022. Benthic exometabolites and their ecological significance on threatened Caribbean coral reefs. ISME Communications. 2:101. Open Access    Press Release

Navarro-Martínez ZM, Armenteros M, Espinosa L, González-Díaz P, Apprill A. 2022. Coral reef ichthyofauna responses poorly to marine protected areas along the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea). PeerJ. 10:e14229 Open Access

Ferguson SR, Jensen FH, Hyer MD, Nobel A, Apprill A, Mooney TA. 2022. Ground-truthing daily and lunar patterns of coral reef fish call rates on a US Virgin Island reef. Aquatic Biology. 31: 77-87.  Open Access

Navarro-Martinez ZM, Armenteros M, Espinosa L, Lake JJ, Apprill A. 2022. Taxonomic and functional assemblage structure of coral reef fishes from Jardines de la Reina (Caribbean Sea, Cuba). Marine Ecology Progress Series. 690:113-132. Link to article

Huntley N, Brandt ME, Becker C, Miller CA, Meiling S, Correa AMS, Holstein D, Muller E, Mydlarz A, Smith TB, Apprill A. 2022. Experimental transmission of Stony Coral Tissue Loss Disease results in differential microbial responses within coral mucus and tissue. ISME Communications. 2:46. Open access

Ma L, Becker C, Weber L, Sullivan C, Zgliczynski B, Sandin S, Brandt M, Smith TB, Apprill A. 2022. Biogeography of reef water microbes from within-reef to global scales. Aquatic Microbial Ecology. 88:81-94.  Link to article

Veglia AJ, Beavers K, Van Buren EW, Meiling SS, Muller EM, Smith TB, Holstein DM, Apprill A, Brandt ME, Mydlarz LD, Correa AMS. 2022. Alphaflexivirus genomes in stony coral tissue loss disease (SCTLD)-affected, disease-exposed and unexposed coral colonies in the U.S. Virgin Islands." Microbiology Resource Announcements 11:e01199-21. Open access

Pereira A, Soares MC, Santos T, Poças A, Pérez-Losada M, Apprill A, Sikkel PC, Xavier R. 2022. Reef Location and Client Diversity Influence the Skin Microbiome of the Caribbean Cleaner Goby Elacatinus evelynae. Microbial Ecology. pp.1-11.  Link to article

Farfan GA, Apprill A, Cohen A, DeCarlo TM, Post JE, Waller RG, Hansel CM. 2022. Crystallographic and chemical signatures in coral skeletal aragonite. Coral Reefs. 41: 19-34. Open access

Becker CC, Brandt M, Miller CA, Apprill A. 2022. Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach. Environmental Microbiology. 24:1166-1182. Link to article


Leray M, Wilkins LG, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy JE, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillian O, O’Dea A, Pereira TJ, Peterson JM, Petticord DF, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA. 2021. Natural experiments and long-term monitoring are critical to understand and predict marine host–microbe ecology and evolution. PLoS Biology. 19:e3001322   Open access

Meiling SS, Muller EM, Lasseigne D, Rossin A, Veglia AJ, MacKnight N, Dimos B, Huntley N, Correa A, Smith TB, Holstein DM, Mydlarz LD, Apprill A, Brandt ME. 2021. Variable species responses to experimental stony coral tissue loss disease (SCTLD) exposure. Frontiers in Marine Science. 8:464. Open access

Bent SM, Miller CA, Sharp KH, Hansel CM, Apprill A. 2021. Differential patterns of microbiota recovery in symbiotic and aposymbiotic corals following antibiotic disturbance. mSystems. e01086-20.  Open access    Press release

Apprill A, Holm H, Santoro A, Becker CC, Neave M, Hughen K, Dona A, Aeby G, Work T, Weber L, McNally S. 2021. Microbial ecology of coral-dominated reefs in the Federated States of Micronesia. Aquatic Microbial Ecology. 86: 115-136. Open access

Keller AG, Apprill A, Lebaron P, Robbins J, Romano TA, Overton E, Rong Y, Yuan R, Pollara S, Whalen KE. 2021. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology. 97: fiab040. Open access

Babbin AR, Tamasi T, Dumit D, Weber L, Rodríguez MVI, Schwartz SL, Armenteros M, Wankel SD, Apprill A. 2021. Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. The ISME Journal. 15:1222-1235.  Open access   Press release


Weber L, Armenteros M, Soule MK, Longnecker K, Kujawinski EB, Apprill A. 2020. Extracellular reef metabolites across the protected Jardines de la Reina, Cuba reef-system. Frontiers in Marine Science. 7:582161. Open access

Van Cise AM, Wade PR, Goertz CEC Burek-Huntington K, Parsons K, Clauss T, Hobbs RC, Apprill A. 2020. Skin microbiome of beluga whales: spatial, temporal and health-related dynamics. Animal Microbiome. 2:39. Open access    Press release

Suca JJ, Lillis A, Jones IT, Kaplan MB, Solow AR, Earl AD, Habtes S, Apprill A, Llopiz JK, Mooney TA. 2020. Variable and spatially explicit response of fish larvae to the playback of local, continuous reef soundscapes. Marine Ecology Progress Series. 653:131-151. Open access

Leslie MS, Perkins-Taylor CM, Durban JW, Moore MJ, Miller CA, Chanarat P, Bahamonde P, Chiang G, Apprill A. 2020. Body size data collected non-invasively from drone images indicate morphologically distinct Chilean blue whales (Balaenoptera musculus Linnaeus 1758). 2020. Endangered Species Research. 43:291-304. Open access

Becker C, Weber L, Suca J, Llopiz JK, Mooney TA, Apprill A. 2020. Microbial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales. Aquatic Microbial Ecology. 85: 101-119. Open access

Apprill A, Miller C, Van Cise A, U’Ren JM, Leslie MS, Weber L, Baird RW, Robbins J, Landry S, Niemeyer M, Rose K, Bogomolni A, Waring G. 2020. Marine mammal skin microbiotas are influenced by host phylogeny. Royal Society of Open Science. 7:192046. Open access

Weber L, Apprill A. 2020. Diel, daily and spatial variation of coral reef seawater microbial communities. PLoS One. 15(3): e0229442. Open access

Apprill A. 2020. The role of symbioses in the adaptation and stress responses of marine organisms. Annual Review of Marine Science. 12:291-314. Link to article

Weber L, González-Diaz P, Armenteros M, Ferrer VM, Bretos F, Bartels E, Santoro AE, Apprill A. 2020. Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys. Environmental Microbiology. 22:499-519. Open access    Press release

Miller CA, Holm HC, Horstmann L, George JC, Fredricks HF, Van Mooy BAS, Apprill A. 2020. Coordinated transformation of the gut microbiome and lipidome of bowhead whales provides novel insights into digestion. The ISME Journal. 14:688-701. Open access    Press release


Grabb, K, Kapit J, Wankel S, Manganini K, Apprill A, Armenteros M, Hansel C. 2019. Quantifying in situ superoxide associated with corals enabled by the development of a handheld submersible chemiluminescent sensor. Environmental Science & Technology. 53:13850-13858. Link to article   Press release

Hernández-Fernández L, González-De Zayas R, Weber L, Apprill A, Armenteros M. 2019. Small-scale variability dominates benthic coverage and diversity across the Jardines de la Reina, Cuba coral reef system. Frontiers in Marine Science. 6:747. Open access

Weber L, Gonzalez-Díaz P, Armenteros M, Apprill A. 2019. The coral ecosphere: a unique coral reef microbial habitat that fosters coral-microbial interactions. Limnology and Oceanography. 64:2373-2388. Open access    Press release

Neave MJ, Apprill A, Aeby G, Miyake S, Voolstra CR. 2019. Microbial communities of Red Sea coral reefs. In Voolstra & Berumen (Eds.), Coral Reefs of the Red Sea (pp. 53). Chaum, Switzerland: Springer.

Apprill A. 2019. On-site sequencing speeds up and re-directs field-based microbiology. Environmental Microbiology Reports. 11:45-47. Link to article

Huggett M, Apprill A. 2019. Coral Microbiome Database: Integration of sequences reveals high diversity and specificity of coral-associated microbes. Environmental Microbiology Reports. 11:372-385. Open access


Lillis A, Apprill A, Suca J, Becker C, Llopiz J, Mooney TA. 2018. Soundscapes influence settlement of the common Caribbean coral Porites astreoides, irrespective of light. Royal Society Open Science. 81358. Open access    Press release

Farfan GA, Apprill A, Webb SM, Hansel CM. 2018. Coupled x-ray fluorescence and x-ray absorption spectroscopy for microscale imaging and identification of sulfur species within tissues and skeletons of scleractinian corals. Analytical Chemistry. 90: 12559–12566. Open access

Dinh JP, Suca JJ, Lillis A, Apprill A, Llopiz J, Mooney TA. 2018. Multiscale spatio-temporal patterns of boat noise on U.S. Virgin Island coral reefs. Marine Pollution Bulletin. 136:292-290. Link to article

Ulmo-Díaz G, Casane D, Bernatchez L, González-Díaz P, Apprill A, Castellanos-Gell J, Hernández-Fernández L, García-Machado E. 2018. Genetic differentiation in the mountainous star coral Orbicella faveolata around Cuba. Coral Reefs. In press Link to article

Bierlich KC, Miller CA, DeForce E, Friedlaender A, Johnston DW, Apprill A. 2018. Temporal and regional variability in the skin microbiomes of humpback whales along the Western Antarctic Peninsula. Applied and Environmental Microbiology. 84:e02574-17. Open access  Cover image!   Press release  Link to taxonomy database


Apprill A, Miller CA, Moore MJ, Durban DW, Fearnbach H, Barrett-Lennard L.G. 2017. Extensive core microbiome in drone-captured whale blow supports a framework for health monitoring. mSystems. 5 e00119-17. Open access  Press release

Becker C, Hughen K, Mincer TJ, Ossolinski J, Weber L, Apprill A. 2017. Impact of prawn framing effluent on coral reef water nutrients and microorganisms. Aquaculture Environmental Interactions. 9:331-346. Open access

Apprill A. 2017. Marine animal microbiomes: toward understanding host-microbiome interactions in a changing ocean. Frontiers in Marine Science. 4:222. Open access

Weber LG, DeForce E, Apprill A. 2017. Optimizing DNA extraction for coral microbiota investigations. Microbiome. 5:18. Open access

Neave MJ, Michell CT, Apprill A, Voolstra CR. 2017 Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Scientific Reports. 7:40579. Open access

McNally SP, Parsons RJ, Santoro AE, Apprill A. 2017. Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition. Limnology and Oceanography. 62:217-234. Open access  Press release

Neave MJ, Rachmawati R, Xun L, Michell CT, Bourne DG, Apprill A, Voolstra CR. 2017. Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales. ISME Journal. 11:186-200. Open access


Diaz J, Hansel C, Apprill A, Brighi C, Zhang T, Weber L, McNally S, Xun L. 2016. Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event. Nature Communications. 7:13801. Open access   Press release

Zhang T, Diaz J, Brighi C, Parsons R, McNally S, Apprill A, Hansel CM. 2016. Dark production of extracellular superoxide by the coral Porites astreoides and representative symbionts. Frontiers in Marine Science. 3:232  Open access

Apprill A, Weber L, Santoro A. 2016. Distinguishing between microbial habitats unravels ecological complexity in coral microbiomes. mSystems. 1 (5) e00143-16. Open access  Editor's Pick!

Neave MJ, Apprill A, Ferrier-Pages C, Voolstra CR. 2016. Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. Applied Microbiology and Biotechnology. 10:8315-8324. Open access

Walters W, Hyde E.R., Berg-Lyons D, Ackermann G, Humphrey G, Parada A, Gilbert J, Jansson JK, Caporaso G, Fuhrman JA, Apprill A, Knight R. 2016. Improved V4, V4-V5 and ITS marker gene primers for microbial community surveys. mSystems. 1(1) e00009-15. Open access

2015 and prior years

Apprill A, McNally SP, Parsons R & Weber L. 2015. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquatic Microbial Ecology. 75:129-137. Open access

Nelson TM, Apprill A, Mann J, Rogers TL, Brown MV. 2015. The marine mammal microbiome: current knowledge and future directions. Microbiology Australia 1:8-13. Open access

Neave MJ, Michell CT, Apprill A, Voolstra CR. 2014. Whole-genome sequencing of three symbiotic Endozoicomonas Bacteria. Genome Announc. 2(4):e00802-14. Open access

Furby KA, Apprill A, Cervino JM, Ossolinski JE, Hughen KA. 2014. Incidence of lesions on Fungiidae corals in the eastern Red Sea is related to water temperature and coastal pollution. Marine Environmental Research. 98: 29-38. Link to article

Apprill A, Robbins J, Eren, AM, Pack AA, Reveillaud J, Mattila D, Moore M, Niemeyer M, Moore KMT, Mincer TJ.  2014. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals? PLOS ONE, e90785. Open access

Reveillaud J, Maignien L, Eren AM, Huber JA, Apprill A, Sogin ML, Vanreusel A. 2014. Host-specificity among abundant and rare taxa in the sponge microbiome. ISME Journal. 9: 1198-1209. Open access

Apprill A, Hughen K, Mincer T. 2013. Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals. Environmental Microbiology. 15: 2063-2072. Open access

Bayer T, Neave M, Alsheikh-Hussain A, Aranda M, Yum L, Mincer T, Hughen K, Apprill A., Voolstra C. 2013. The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria, Applied and Environmental Microbiology. 79:4759-4762.  Open access

Selph KE, Apprill A, Measures CI, Hatta M, Hiscock WT, Brown MT. 2013. Phytoplankton distributions in the Shackleton Fracture Zone/Elephant Island Region of the Drake Passage in February-March 2004. Deep Sea Research II. 90: 55-67. Link to article

Measures CI, Brown MT, Selph KE, Apprill A, Zhou M, Hatta M, Hiscock MT. 2013. The Influence of Shelf Processes in Delivering Dissolved Iron to the HNLC waters of the Drake Passage, Antarctica. Deep Sea Research II. 90: 77-88.  Link to article

Apprill A, Marlow HQ, Martindale MQ, Rappé MS. 2012. Specificity of bacteria associated with the coral Pocillopora meandrina during early development. Applied and Environmental Microbiology. 78: 7467-7475. Link to article

Kahng S, Hochberg EJ, Apprill A, Wagner D, Luck DG, Perez D, Bidigare RR. 2012. Efficient light harvesting in deep-water, zooxanthellate corals.  Marine Ecology Progress Series. 455: 65 -77. Link to article

Apprill A, Rappé MS. 2011. Microbial community response to organic matter loading from coral spawning at lagoon and reef flat environments in Kaneohe Bay. Aquatic Microbial Ecology. 62: 251-266. Open access

Apprill A, Mooney TA, Lyman E, Stimpert AK, Rappé MS. 2011. Humpback whales harbor a combination of specific and variable skin bacteria. Environmental Microbiology Reports. 3: 223-323. Link to article

Apprill A, Marlow HQ, Martindale MQ, Rappé MS. 2009. The onset of microbial associations in the coral Pocillopora meandrina. The ISME Journal. 3: 685-699. Link to article

Hiscock MR, Lance VP, Apprill A, Bidigare RR, Johnson ZI, Mitchell BG, Smith, Jr. WO, Barber RT. 2008. Photosynthetic maximum quantum yield increases are an essential component of the Southern Ocean phytoplankton response to iron. PNAS. 105: 4775-4780. Link to article

Apprill A, Bidigare RR, Gates RD. 2007. Visibly healthy corals exhibit variable pigment concentrations and symbiont phenotypes. Coral Reefs. 26: 387-397. Link to article

Apprill A, and Gates RD. 2007. Recognizing diversity in coral symbiotic dinoflagellate communities. Molecular Ecology 16: 1127-1134. Link to article    Featured article

Hochberg EJ, Apprill A, Bidigare RR, Atkinson MJ. 2006. Bio-optical modeling of photosynthetic pigments in corals. Coral Reefs 25: 99-109. Link to article

Hochberg EJ, Atkinson MJ, Apprill A, Andréfouët S. 2004. Spectral reflectance of coral. Coral Reefs 23: 84-95. Link to article

Apprill A, Lesser MP. 2003. Effects of ultraviolet radiation on Laminaria saccharina in relation to depth and tidal height in the Gulf of Maine. Marine Ecology Progress Series. 256: 75-85. Link to article

Related Files

SSU rRNA gene reference database for Bierlich et al. in review

This is a SSU rRNA gene reference database based off SILVA release v. 123, with additional sequences within the Tenacibaculum and Psychrobacter genera included.  The zip file includes a .tax and .align file, and it inended for use with the mothur analysis pipeline.